4NYF | pdb_00004nyf

HIV integrase in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4NYF/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 lw12.3 isolate
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-12-10 Released: 2014-06-25 
• Deposition Author(s): Coulombe, R., Fader, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor) 
• R-Value Work: 
  0.201 (Depositor), 0.207 (DCC) 

Starting Model: experimental

Literature

Discovery of BI 224436, a Noncatalytic Site Integrase Inhibitor (NCINI) of HIV-1.

Fader, L.D., Malenfant, E., Parisien, M., Carson, R., Bilodeau, F., Landry, S., Pesant, M., Brochu, C., Morin, S., Chabot, C., Halmos, T., Bousquet, Y., Bailey, M.D., Kawai, S.H., Coulombe, R., LaPlante, S., Jakalian, A., Bhardwaj, P.K., Wernic, D., Schroeder, P., Amad, M., Edwards, P., Garneau, M., Duan, J., Cordingley, M., Bethell, R., Mason, S.W., Bos, M., Bonneau, P., Poupart, M.A., Faucher, A.M., Simoneau, B., Fenwick, C., Yoakim, C., Tsantrizos, Y.

(2014) ACS Med Chem Lett 5: 422-427

• PubMed: 24900852 
• DOI: https://doi.org/10.1021/ml500002n
• Primary Citation Related Structures: 
  4NYF


• PubMed Abstract: 
  

  An assay recapitulating the 3' processing activity of HIV-1 integrase (IN) was used to screen the Boehringer Ingelheim compound collection. Hit-to-lead and lead optimization beginning with compound 1 established the importance of the C3 and C4 substituent to antiviral potency against viruses with different aa124/aa125 variants of IN. The importance of the C7 position on the serum shifted potency was established. Introduction of a quinoline substituent at the C4 position provided a balance of potency and metabolic stability. Combination of these findings ultimately led to the discovery of compound 26 (BI 224436), the first NCINI to advance into a phase Ia clinical trial.

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Organizational Affiliation: 
• Research and Development, Boehringer Ingelheim (Canada) Ltd. , 2100 Cunard Street, Laval, Québec H7S 2G5, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.18 kDa 
• Atom Count: 2,419 
• Modeled Residue Count: 289 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	168	Human immunodeficiency virus type 1 lw12.3 isolate	Mutation(s): 4  Gene Names: gag-pol EC: 2.7.7
UniProt
Find proteins for P0C6F2 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123)) Explore P0C6F2  Go to UniProtKB:  P0C6F2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4BI	C [auth A]	(2S)-tert-butoxy[4-(4-chlorophenyl)-2-methylquinolin-3-yl]ethanoic acid C22 H22 Cl N O3 BCLKGXWEVQRUHG-FQEVSTJZSA-N
CD	D [auth A], E [auth A], F [auth B], G [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.223 (Depositor) 
• R-Value Work:  0.201 (Depositor), 0.207 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.77	α = 90
b = 62.45	β = 90
c = 81.32	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Coulombe, R., Fader, L.

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description